The parallel computing of a molecular docking algorithm using the JavaSpaces service

The molecular docking is the focus of practical applications such as protein engineering and drug design. A docking algorithm is a procedure that predicts the assembly of two molecules like a key and a lock. To screen a large library of molecules, a docking algorithm requires high performance computing. Parallel and distributed applications have long been recognized as powerful computational tools and effective in the field of bioinformatics. Jini technology is one of the powerful infrastructures network for building and deploying distributed systems that are organized as a federation of services. JavaSpaces is one of the services that come bundled with Jini, it is a shared associative memory accessible by the network and allows an easily developing of a massively parallel and distributed applications. This paper discusses the use of the JavaSpaces service to build a distributed application in order to minimize the running time of a molecular docking algorithm.